2QM2 | pdb_00002qm2

Putative HopJ type III effector protein from Vibrio parahaemolyticus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QHQPDB entry 2QHQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.62950.4M NaH2PO4, 1.6M K2HPO4, 0.1M Imidazole pH 8.0, 0.2M NaCl pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5451.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.622α = 90
b = 90.886β = 90
c = 72.445γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97930APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0950890.11114.510.11550115501
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.092.1855.60.2247.27.3958

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT, SADTHROUGHOUTPDB entry 2QHQ2.0938.491391513915157088.720.2170.2170.2090.210.2810.28RANDOM42.718
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.24-3.922.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.372
r_dihedral_angle_3_deg20.209
r_dihedral_angle_4_deg20.168
r_dihedral_angle_1_deg6.855
r_scangle_it4.503
r_scbond_it3.008
r_angle_refined_deg1.773
r_mcangle_it1.584
r_mcbond_it0.863
r_nbd_refined0.264
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1855
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing